scout-browser 4.80__py3-none-any.whl → 4.82.1__py3-none-any.whl

scout/server/blueprints/cases/templates/cases/chanjo2_form.html

@@ -0,0 +1,47 @@
+{% macro chanjo2_report_form(institute_obj, case_obj, panel_name, report_type, hgnc_ids, link_text) %}
+
+  {% set form_name = "chanjo2_"+panel_name+"_"+report_type %}
+  {% set form_action = config.CHANJO2_URL+"/"+report_type %}
+  {% set build = "GRCh38" if "38" in case_obj.get("genome_build", "37") else "GRCh37" %}
+  {% set default_level = institute_obj.coverage_cutoff %}
+  {% set interval_type = "genes" %} <!-- wgs analysis as default -->
+  {% set samples = [] %}
+  {% set analysis_types = [] %}
+
+  <!-- set sample dictionaries -->
+
+  {% for ind in case_obj.individuals %}
+    {% if ind.d4_file %}
+      {% set sample = {
+        "name" : ind.display_name,
+        "coverage_file_path" : ind.d4_file,
+        "case_name" : case_obj.display_name,
+        "analysis_date" : case_obj.analysis_date.strftime("%FT%T.%f")[:-3] ~ "Z" }
+      %}
+      {% do samples.append( sample ) %}
+      {% do analysis_types.append( ind.analysis_type ) %}
+    {% endif %}
+  {% endfor %}
+
+  {% if "wes" in analysis_types %}
+    {% set interval_type = "exons" %}
+  {% elif "wts" in analysis_types %}
+    {% set interval_type = "transcripts" %}
+  {% endif %}
+
+  <form name="{{form_name}}" method="post" action="{{form_action}}" target="_blank" rel="noopener">
+    <input type="hidden" id="build" name="build" value="{{build}}">
+    <input type="hidden" id="default_level" name="default_level" value="{{default_level}}">
+    <input type="hidden" id="interval_type" name="interval_type" value="{{interval_type}}">
+    <input type="hidden" id="panel_name" name="panel_name" value="{{panel_name}}">
+    <input type="hidden" id="case_display_name" name="case_display_name" value="{{case_obj.display_name}}">
+    <input type="hidden" id="hgnc_gene_ids" name="hgnc_gene_ids" value={{hgnc_ids}}>
+    <input type="hidden" id="samples" name="samples" value="{{samples|safe}}">
+    {% if panel_name == "HPO Panel" %}
+      <button type="submit" class="btn btn-secondary btn-sm text-white"> Coverage {{report_type}} (Chanjo2) </button>
+    {% else %}
+      <a class="link-primary" onclick="this.closest('form').submit();return false;">{{link_text}}</a>
+    {% endif %}
+  </form>
+
+{% endmacro %}

scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html

@@ -1,3 +1,5 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
+
 {% macro action_bar(institute, case, causatives, collaborators, current_user, report_types, has_rna_tracks) %}
 <!-- Collapsible Sidebar, Based on https://www.codeply.com/go/LFd2SEMECH -->
   <div id="sidebar-container" class="sidebar-expanded d-none d-md-block"><!-- d-* hiddens the Sidebar in smaller devices. Its itens can be kept on the Navbar 'Menu' -->
@@ -84,13 +86,11 @@
     </div>
 
     <!-- If connected to a chanjo or chanjo2 instance, display coverage report -->
-    {% if case.chanjo2_coverage %}
+    {% if case.chanjo2_coverage and case.default_genes %}
       <div href="#" class="bg-dark list-group-item text-white">
         <div class="d-flex flex-row flex-fill bd-highlight">
           <span class="menu-collapsed">Coverage (chanjo2)</span>
-          <a href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id, case_name=case.display_name, panel_name=case.panel_names|join(', '), report_type='report') }}" target="_blank" rel="noopener">
-            <span class="fa fa-link"></span>
-          </a>
+          {{ chanjo2_report_form(institute, case, case.panel_names|join(', '), 'report', case.default_genes|join(','), "<span class='fa fa-link'></span>"|safe ) }} <!--chanjo2 report-->
         </div>
       </div>
     {% endif %}

scout/server/blueprints/cases/templates/cases/gene_panel.html

@@ -1,3 +1,5 @@
+{% from "cases/chanjo2_form.html" import chanjo2_report_form %}
+
 {% macro genepanels_table(case, institute) %}
   <div class="card panel-default">
     <div class="panel-heading">Gene panels</div>
@@ -130,8 +132,8 @@
         </div>
       </div>
 
-      <div class="row mt-2"> <!-- Show variants in dynamic gene list -->
-        <div class="row">
+      <div>
+        <div class="row"> <!-- Show variants in dynamic gene list -->
           <form action="{{ url_for('cases.update_clinical_filter_hpo', institute_id=institute._id, case_name=case.display_name)+'#hpo_clinical_filter' }}" method="POST">
             <div class="form-check form-switch">
               <input type="checkbox" class="form-check-input" id="hpo_clinical_filter" onChange="this.form.submit()" name="hpo_clinical_filter"{% if case.hpo_clinical_filter %}checked{% endif %}>
@@ -199,41 +201,33 @@
         <div class="row mt-1">
           <div class="btn-group btn-group-sm">
             {% if case.chanjo_coverage %}
-              <button class="btn btn-secondary btn-sm text-white" onClick="document.getElementById('hpo-report-form').submit();">Coverage report</button>
-              <a href="#section" onClick="document.getElementById('hpo-report-form').submit();" />
-              <form id="hpo-report-form" action="{{ url_for('report.report', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name="HPO panel", level=institute.coverage_cutoff) }}" method="POST" target="_blank">
+              <a class="btn btn-secondary btn-sm text-white" href="#section" onClick="document.getElementById('hpo-report-form').submit();" >Coverage report</a>
+              <form id="hpo-report-form" action="{{ url_for('report.report', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name='HPO panel', level=institute.coverage_cutoff) }}" method="POST" target="_blank">
                 <input type="hidden" name="gene_ids" value="{{ case.dynamic_gene_list|map(attribute='hgnc_id')|join(',') }}">
               </form>
 
-              <button class="btn btn-secondary btn-sm text-white" onClick="document.getElementById('hpo-overview-form').submit();">Coverage overview</button>
-              <a href="#section" onClick="document.getElementById('hpo-overview-form').submit();" />
-              <form id="hpo-overview-form" action="{{ url_for('report.genes', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name="HPO panel", level=institute.coverage_cutoff) }}" method="POST" target="_blank">
+              <a class="btn btn-secondary btn-sm text-white" href="#section" onClick="document.getElementById('hpo-overview-form').submit();" >Coverage overview</a>
+              <form id="hpo-overview-form" action="{{ url_for('report.genes', sample_id=case.individuals|map(attribute='individual_id')|list, panel_name='HPO panel', level=institute.coverage_cutoff) }}" method="POST" target="_blank">
                 <input type="hidden" name="gene_ids" value="{{ case.dynamic_gene_list|map(attribute='hgnc_id')|join(',') }}">
               </form>
             {% endif %}
 
             {% if case.chanjo2_coverage %}
-              <a class="btn btn-secondary btn-sm text-white"
-                href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id,
-                                 case_name=case.display_name, panel_name='HPO Panel', report_type='report') }}" target="_blank" rel="noopener">
-                  Coverage report (Chanjo2)
-              </a>
-
-              <a class="btn btn-secondary btn-sm text-white"
-                href="{{ url_for('cases.chanjo2_coverage_report', institute_id=institute._id,
-                                 case_name=case.display_name, panel_name='HPO Panel', report_type='overview') }}" target="_blank" rel="noopener">
-                  Coverage overview (Chanjo2)
-              </a>
+              {{ chanjo2_report_form(institute, case, "HPO Panel", 'report', case.dynamic_gene_list|map(attribute='hgnc_id')|join(',')) }} <!--chanjo2 report-->
+              {{ chanjo2_report_form(institute, case, "HPO Panel", 'overview', case.dynamic_gene_list|map(attribute='hgnc_id')|join(',')) }} <!--chanjo2 genes overview -->
             {% endif %}
 
           </div>
         </div>
         {% endif %} <!-- End of if case.chanjo_coverage or case.chanjo2_coverage -->
-      </div> <!-- End of Show variants in dynamic gene list -->
 
-      <div class="btn-group d-flex justify-content-center mt-1"> <!-- Download genes in HPO gene panel -->
-        <a class="btn btn-sm btn-primary text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="clinical") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Clinical HPO gene panel</a>
-        <a class="btn btn-sm btn-primary text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="research") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Research HPO gene panel</a>
+        <div class="row mt-1">
+          <div class="btn-group btn-group-sm"> <!-- Download genes in HPO gene panel -->
+            <a class="btn btn-sm btn-primary text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="clinical") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Clinical HPO gene panel</a>
+            <a class="btn btn-sm btn-primary text-white" href="{{ url_for('cases.download_hpo_genes', institute_id=institute._id, case_name=case.display_name, category="research") }}" download><span class="fa fa-download text-white" aria-hidden="true"></span>&nbsp;&nbsp;Research HPO gene panel</a>
+          </div>
+        </div>
+
       </div>
 
     {% endif %}

scout/server/blueprints/cases/templates/cases/utils.html

@@ -268,7 +268,7 @@
 
         <!-- show transcript info only if it's canonical, disease-associated or primary (print max 5 primary transcripts) -->
       {% if transcript.refseq_identifiers and n_primary_txs.count <= 5 or transcript.is_canonical or transcript.is_disease_associated or transcript.is_primary %}
-        <li>{{transcript.transcript_id}}, RefSeq:[{{ transcript.refseq_identifiers|join(", ") or "-" }}], {{ (transcript.coding_sequence_name or '')|truncate(20, True) }},  {{ (transcript.protein_sequence_name or '')|url_decode|truncate(20, True) }}
+        <li class="mb-1">{{transcript.transcript_id}}, RefSeq:[{{ transcript.refseq_identifiers|join(", ") or "-" }}], {{ (transcript.coding_sequence_name or '')|truncate(20, True) }},  {{ (transcript.protein_sequence_name or '')|url_decode|truncate(20, True) }}
           {% if transcript.is_canonical %}
             <span class="badge rounded-pill bg-info text-white" title="canonical">C</span>
           {% endif %}
@@ -602,6 +602,8 @@
         <form id="clinvar_submit" class="d-flex justify-content-center" action="{{ url_for('clinvar.clinvar_add_variant', institute_id=institute._id, case_name=case.display_name) }}" method="POST">
             {% if case.clinvar_variants and variant._id in case.clinvar_variants.keys() %}
                 (included in ClinVar submission)
+            {% elif variant.category in ('cancer', 'cancer_sv') %}
+                <button data-bs-toggle='tooltip' data-bs-placement="bottom" title="Submission of somatic variants from Scout is temporarily suspended. We are working to harmonize submissions with changes introduced by ClinVar for this variant category." disabled >Add to ClinVar submission</button>
             {% else %}
                 <button type="submit" name="var_id" value="{{variant._id}}" class="btn btn-secondary btn-sm" style="float: right;">Add to ClinVar submission</button>
             {% endif %}

scout/server/blueprints/cases/views.py

@@ -313,28 +313,6 @@ def pdf_case_report(institute_id, case_name):
     )
 
 
-@cases_bp.route("/<institute_id>/<case_name>/chanjo2_report/<report_type>", methods=["GET"])
-def chanjo2_coverage_report(institute_id: str, case_name: str, report_type: str):
-    """Return the HTML coverage report or coverage overview created by chanjo2."""
-
-    REPORT_TYPES = ["report", "overview"]
-    if report_type not in REPORT_TYPES:
-        flash(f"Wrong value for report_type parameter. Accepted values: {REPORT_TYPES}", "warning")
-        return redirect(request.referrer)
-
-    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
-    report_html_content: str = controllers.chanjo2_coverage_report_contents(
-        institute_obj=institute_obj,
-        case_obj=case_obj,
-        panel_name=request.args.get("panel_name"),
-        panel_id=request.args.get("panel_id"),
-        report_type=report_type,
-    )
-    if report_html_content is None:
-        return redirect(request.referrer)
-    return report_html_content
-
-
 @cases_bp.route("/<institute_id>/<case_name>/mt_report", methods=["GET"])
 def mt_report(institute_id, case_name):
     institute_obj, case_obj = institute_and_case(store, institute_id, case_name)

scout/server/blueprints/clinvar/controllers.py

@@ -107,7 +107,7 @@ def _get_snv_var_form(variant_obj, case_obj):
     var_form.variations_ids.data = var_ids.split(";")[0]
     var_form.chromosome.data = variant_obj.get("chromosome")
     var_form.start.data = variant_obj.get("position")
-    var_form.stop.data = variant_obj.get("position")
+    var_form.stop.data = variant_obj.get("end")
     return var_form
 
 
@@ -276,7 +276,7 @@ def parse_variant_form_fields(form):
         clinvar_var["variations_ids"] = form["dbsnp_id"]
 
     if clinvar_var.get("ref_seq") and clinvar_var.get("hgvs"):
-        # Variant is described by RefSeq and HGVS already, remove redundanti fields from submission
+        # Variant is described by RefSeq and HGVS already, remove redundant fields from submission
         for item in ["chromosome", "start", "stop", "ref", "alt"]:
             clinvar_var.pop(item)
 
@@ -437,7 +437,7 @@ def send_api_submission(institute_id, submission_id, key):
 
     clinvar_id = store.get_clinvar_id(
         submission_id
-    )  # This is the official ID associated with this submission in Clinvar ((ex: SUB999999)
+    )  # This is the official ID associated with this submission in Clinvar (ex: SUB999999)
 
     if clinvar_id:  # Check if submission object has already an associated ClinVar ID
         conversion_res["submissionName"] = clinvar_id

scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html

@@ -95,10 +95,16 @@
               </form>
               {% if subm_obj.status == 'open' and show_submit  %}
                 <form id="useApi_{{subm_obj._id}}" action="{{ url_for('clinvar.clinvar_update_submission', institute_id=institute._id, submission=subm_obj._id) }}" method="POST">
-                {{ submit_modal(subm_obj) }}
+                {{ submit_modal() }}
                   <td style="width: 20%"><button type="button" class="btn btn-sm btn-success form-control" name="update_submission" value="api_submit" data-bs-toggle="modal" data-bs-target="#submitModal">Submit to ClinVar</button></td>
                 </form>
               {% endif %}
+              {% if subm_obj.status == 'submitted' %} <!--Submission status query -->
+                 <form id="statusApi_{{subm_obj._id}}" action="{{ url_for('clinvar.clinvar_submission_status', submission_id=subm_obj.clinvar_subm_id) }}" method="POST">
+                   {{ status_modal() }}
+                   <td style="width: 20%"><button type="button" class="btn btn-sm btn-secondary form-control" name="status_enquiry" value="api_status" data-bs-toggle="modal" data-bs-target="#statusModal">Submission status enquiry</button></td>
+                 </form>
+              {% endif %}
             </tr>
           </table>
         </div>
@@ -240,7 +246,28 @@
 </div>
 {% endmacro %}
 
-{% macro submit_modal(subm_obj) %}
+{% macro status_modal() %}
+<div class="modal fade" id="statusModal" tabindex="-1">
+  <div class="modal-dialog">
+    <div class="modal-content">
+      <div class="modal-header">
+        <h5 class="modal-title">Submission status</h5>
+        <button type="button" class="btn-close" data-bs-dismiss="modal" aria-label="Close"></button>
+      </div>
+      <div class="modal-body">
+        <label for="apiKey">Submitter's <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/" target="_blank" rel="noopener">API key</a></label>
+        <input type="password" class="form-control" name="apiKey" id="apiKey" placeholder="64 alphanumeric characters" value="{{institute.clinvar_key or ''}}" required>
+      </div>
+      <div class="modal-footer">
+        <button type="button" class="btn btn-secondary" data-bs-dismiss="modal">Close</button>
+        <button type="submit" name="show_status" value="status" class="btn btn-primary">Submission status enquiry</button>
+      </div>
+    </div>
+  </div>
+</div>
+{% endmacro %}
+
+{% macro submit_modal() %}
 <div class="modal fade" id="submitModal" tabindex="-1">
   <div class="modal-dialog">
     <div class="modal-content">

scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html

@@ -34,7 +34,7 @@
               </ul>
               <!-- fieldsets -->
               <fieldset data-step="1">
-                <legend>ClinVar variant submission form</legend>
+                <legend class="text-dark">ClinVar variant submission form</legend>
                 <p class="text-dark">
                 The form present on this page mirrors the fields on the ClinVar submission spreadsheets.<br>
                 After collecting the required fields, this variant gets saved in an open ClinVar submission object.<br>
@@ -44,7 +44,7 @@
               </fieldset>
 
               <fieldset data-step="2">
-                <legend>Assertion criteria <span class="text-danger" data-bs-toggle='tooltip' title="The new ClinVar spreadsheet templates (versions L1.7 and 4.3) no longer include the following columns: Assertion method and Assertion method citation.
+                <legend class="text-dark">Assertion criteria <span class="text-danger" data-bs-toggle='tooltip' title="The new ClinVar spreadsheet templates (versions L1.7 and 4.3) no longer include the following columns: Assertion method and Assertion method citation.
                   New files for assertion criteria will be uploaded on your landing page in the ClinVar Submission Portal, independent of a submission. For this reason Scout will collect this information but will not export it as columns in the submission Variant file."><strong>?</strong></span></legend>
 
                 <!-- hidden fields -->
@@ -73,7 +73,7 @@
                   <br><br>
                   <div class="d-flex flex-column flex-lg-row justify-content-center align-items-center">
                   {{variant_data.var_form.assertion_method_cit_db.label(class="fw-bold text-dark my-2 mx-lg-2")}}
-                  {{variant_data.var_form.assertion_method_cit_db(class="bg-white my-2 mx-lg-2")}}
+                  {{variant_data.var_form.assertion_method_cit_db(class="btn-secondary my-2 mx-lg-2")}}
                   <div class="my-2 mx-lg-2">{{variant_data.var_form.assertion_method_cit_id.label(class="fw-bold text-dark")}}
                     <span class="text-danger" id="assertion_method_cit_id_tooltip"  data-bs-toggle='tooltip' title="The Assertion method citation is now supplied as a database identifier and an id number in the corresponding format">
                       <strong>?</strong>
@@ -85,7 +85,7 @@
                 <input type="button" name="next" class="next action-button" value="Next"/>
               </fieldset>
               <fieldset data-step="3">
-                  <legend>Variant Details</legend>
+                  <legend class="text-dark">Variant Details</legend>
                   {{variant_data.var_form.gene_symbol.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Gene symbol should be provided only to indicate the gene-disease relationship supporting the variant interpretation. Gene symbol is not expected for SVs, except to make a statement that a specific gene within the variant has a relationship to the interpreted condition."><strong>?</strong></span>
                   {{variant_data.var_form.gene_symbol(class="bg-white")}}
                   <br>
@@ -114,7 +114,7 @@
                     {% for item_row in variant_data.var_form.tx_hgvs | batch(3) %}
                       <tr>
                       {% for item in item_row %}
-                        <td style="width: 3%; text-align: right; vertical-align: baseline;">{{item()}}</td>
+                        <td style="width: 3%; text-align: right; vertical-align: baseline;">{{item}}</td>
 
                         {% if "(validated)" in item.label.text %}
                           {% set ns.validated = true %}
@@ -124,7 +124,7 @@
                         {% set ns.label = item.label.text | replace(" (validated)", "") %}
 
                         <td style="width: 30%; text-align: left; ">
-                          <p
+                          <p class="text-dark"
                           {% if ns.label|length > 25 %}
                            data-bs-toggle="tooltip" title="{{ns.label}}">{{ ns.label|truncate(25,true,'..') }}
                           {% else %}
@@ -196,7 +196,7 @@
               </fieldset>
 
               <fieldset data-step="4">
-                <legend>Inheritance model</legend>
+                <legend class="text-dark">Inheritance model</legend>
                 <h3 class="fs-subtitle">The mode of inheritance specific to the variant-disease pair, not generally for the disease</h3>
                 {{variant_data.var_form.inheritance_mode.label(class="fw-bold, text-dark")}}
                 {{variant_data.var_form.inheritance_mode(class="form-control, btn-secondary")}}
@@ -206,7 +206,7 @@
               </fieldset>
 
               <fieldset data-step="5">
-                <legend>Germline Classification</legend>
+                <legend class="text-dark">Germline Classification</legend>
                 <h3 class="fs-subtitle">Represents a variant-level classification for a disease, rather than an interpretation of the clinical significance of a variant for a specific patient.</h3>
 
                 <div class="row">
@@ -231,23 +231,19 @@
               </fieldset>
 
               <fieldset data-step="6">
-                <legend>Associated Conditions</legend>
+                <legend class="text-dark">Associated Conditions</legend>
                 <h3 class="fs-subtitle">The condition for which the variant is interpreted. Examples available at <a href="https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#condition" target="_blank" rel="noopener">ClinVar</a></h3>
 
                 <div class="row">
                   <div class="col-6" id="clinvar_condition_container">
                     {{variant_data.var_form.condition_type.label(class="fw-bold, text-dark")}}<span class="text-danger" data-bs-toggle='tooltip' title="Required field."><strong>*</strong></span>
+
                     <select class="form-control, btn-secondary" name="condition_type" id="condition_type">
                       {% for dbtype, _ in variant_data.var_form.condition_type.choices %}
-                        {% if dbtype == "OMIM" and variant_data.var_form.omim_terms.choices %}
-                          <option value="{{dbtype}}" selected>{{dbtype}}</option>
-                        {% elif dbtype == "HP" and variant_data.var_form.hpo_terms.choices %}
-                          <option value="{{dbtype}}" selected>{{dbtype}}</option>
-                        {% else %}
-                          <option value="{{dbtype}}">{{dbtype}}</option>
-                        {% endif %}
+                        <option value="{{dbtype}}">{{dbtype}}</option>
                       {% endfor %}
                     </select>
+
                     <br><br>
                     {{variant_data.var_form.conditions.label(class="fw-bold, text-dark")}} <span class="text-danger" data-bs-toggle='tooltip' title="Required field. Include data from ONE DATABASE TYPE ONLY (i.e. only OMIM terms, only HPO terms etc). If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s).  i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records."><strong>*?</strong></span>
                     <select class="select2" id="condition_tags" name="conditions" multiple="true" style="width:100%;">
@@ -313,7 +309,7 @@
               </fieldset>
 
               <fieldset data-step="7">
-                <legend>Observation Data</legend>
+                <legend class="text-dark">Observation Data</legend>
                 <h3 class="fs-subtitle">Information provided by filling in these fields will be used to create the CaseData.csv file. Observations from at least one individuals are required.</h3>
 
                 <ul class="list-group">
@@ -372,6 +368,7 @@ var tooltipList = tooltipTriggerList.map(function (tooltipTriggerEl) {
 
 // Validates fields for conditions associated to a variant
 function validateConditions(){
+
   if ($("#condition_tags option:selected").length == 0) {
     alert("Please provide at least one condition ID");
     return false;
@@ -387,7 +384,16 @@ function validateConditions(){
     return false;
   }
 
-  return true
+  // Make sure that provided conditions are numbers, except when condition type is MeSH
+  var selectedConditionsValues = $('#condition_tags').val();
+  for (let i = 0; i < selectedConditionsValues.length; i++) {
+    if (isNaN(selectedConditionsValues[i]) && $('#condition_type').val() != 'MeSH'){
+      alert(`Condition ID "${selectedConditionsValues[i]}" has an invalid format.`);
+      return false;
+    }
+  }
+
+  return true;
 }
 
 var current_fs, next_fs, previous_fs; //fieldsets
@@ -526,6 +532,18 @@ $('#condition_tags').select2({
   allowClear: true,
 });
 
+// Set selected condition type on page load
+window.onload = function() {
+  const selectedCondId = document.getElementById('condition_type');
+  {% if variant_data.var_form.omim_terms.choices %}
+    selectedCondId.options.selectedIndex = 4;
+  {% elif variant_data.var_form.orpha_terms.choices %}
+    selectedCondId.options.selectedIndex = 5;
+  {% elif variant_data.var_form.hpo_terms.choices %}
+    selectedCondId.options.selectedIndex = 0;
+  {% endif %}
+};
+
 // reset and modify conditions field's placeholder when condition ID type changes
 $(function(){
   $("#condition_type").change(function(){

scout/server/blueprints/clinvar/views.py

@@ -8,7 +8,7 @@ from flask import Blueprint, flash, redirect, render_template, request, send_fil
 from flask_login import current_user
 
 from scout.constants.clinvar import CASEDATA_HEADER, CLINVAR_HEADER, GERMLINE_CLASSIF_TERMS
-from scout.server.extensions import store
+from scout.server.extensions import clinvar_api, store
 from scout.server.utils import institute_and_case
 
 from . import controllers
@@ -24,6 +24,18 @@ clinvar_bp = Blueprint(
 )
 
 
+@clinvar_bp.route("/clinvar/status-enquiry/<submission_id>", methods=["POST"])
+def clinvar_submission_status(submission_id):
+    """Sends a request to ClinVar to retrieve and display the status of a submission."""
+
+    # flash a message with current submission status for a ClinVar submission
+    clinvar_api.show_submission_status(
+        submission_id=submission_id, api_key=request.form.get("apiKey")
+    )
+
+    return redirect(request.referrer)
+
+
 @clinvar_bp.route("/<institute_id>/<case_name>/clinvar/add_variant", methods=["POST"])
 def clinvar_add_variant(institute_id, case_name):
     """Create a ClinVar submission document in database for one or more variants from a case."""

scout/server/blueprints/diagnoses/controllers.py

@@ -36,6 +36,8 @@ def disease_terms(store: MongoAdapter, query: str, source: str) -> dict:
 
         for gene in gene_ids:
             gene_caption = store.hgnc_gene_caption(hgnc_identifier=gene)
+            if not gene_caption:
+                continue
             gene_ids_symbols.append(
                 {"hgnc_id": gene_caption["hgnc_id"], "hgnc_symbol": gene_caption["hgnc_symbol"]}
             )

scout/server/blueprints/institutes/controllers.py

@@ -469,7 +469,12 @@ def cases(store, request, institute_id):
 
     data["status_ncases"] = store.nr_cases_by_status(institute_id=institute_id)
     data["nr_cases"] = sum(data["status_ncases"].values())
-    data["sanger_unevaluated"] = get_sanger_unevaluated(store, institute_id, current_user.email)
+
+    sanger_ordered_not_validated: Tuple[Dict[str, list]] = get_sanger_unevaluated(
+        store, institute_id, current_user.email
+    )
+    data["sanger_unevaluated"]: Dict[str, list] = sanger_ordered_not_validated[0]
+    data["sanger_validated_by_others"]: Dict[str, list] = sanger_ordered_not_validated[1]
 
     # local function to add info to case obj
     def populate_case_obj(case_obj):
@@ -559,27 +564,76 @@ def populate_case_filter_form(params):
     return form
 
 
-def get_sanger_unevaluated(store, institute_id, user_id):
-    """Get all variants for an institute having Sanger validations ordered but still not evaluated
+def _get_unevaluated_variants_for_case(
+    case_obj: dict, var_ids_list: List[str], sanger_validated_by_user_by_case: Dict[str, List[str]]
+) -> Tuple[Dict[str, list]]:
+    """Returns the variants with Sanger ordered by a user that need validation or are validated by another user."""
 
-    Args:
-        store(scout.adapter.MongoAdapter)
-        institute_id(str)
+    case_display_name: str = case_obj["display_name"]
+    case_id: str = case_obj["_id"]
+
+    def _variant_has_sanger_ordered(variant_obj: dict) -> bool:
+        """Returns True if the sanger_ordered status of a variant is True, else False."""
+
+        if (
+            variant_obj is None
+            or variant_obj.get("sanger_ordered") is None
+            or variant_obj.get("sanger_ordered") is False
+        ):
+            return False
+        return True
+
+    unevaluated_by_case = {case_display_name: []}
+    evaluated_by_others_by_case = {case_display_name: []}
+    for var_id in var_ids_list:
+        # For each variant with sanger validation ordered
+        variant_obj = store.variant(document_id=var_id, case_id=case_id)
+
+        # Double check that Sanger was ordered (and not canceled) for the variant
+        if _variant_has_sanger_ordered(variant_obj) is False:
+            continue
+
+        validation = variant_obj.get("validation", "not_evaluated")
+
+        # Check that the variant is not evaluated
+        if validation in ["True positive", "False positive"]:
+            if var_id in sanger_validated_by_user_by_case.get(
+                case_id, []
+            ):  # User had validated this variant
+                continue
+
+            # Another user has validated the variant
+            evaluated_by_others_by_case[case_display_name].append(variant_obj["_id"])
+        else:
+            unevaluated_by_case[case_display_name].append(variant_obj["_id"])
+
+    return unevaluated_by_case, evaluated_by_others_by_case
+
+
+def get_sanger_unevaluated(
+    store: MongoAdapter, institute_id: str, user_id: str
+) -> Tuple[List[Dict[str, list]]]:
+    """Return all variant with Sanger sequencing ordered by a user with validation missing or validated by another user.
 
     Returns:
-        unevaluated: a list that looks like this: [ {'case1': [varID_1, varID_2, .., varID_n]}, {'case2' : [varID_1, varID_2, .., varID_n]} ],
+        unevaluated: a list that looks like this: [ {'case1': [varID_1, varID_2, .., varID_n]}, .. ],
                      where the keys are case_ids and the values are lists of variants with Sanger ordered but not yet validated
+        evaluated_by_others: a list that looks like the one above where varID_1, varID_2 etc are variants validated by some other user
 
     """
+    sanger_ordered_by_user_by_case: Dict[str, List[str]] = {
+        case_variants["_id"]: case_variants["vars"]
+        for case_variants in store.sanger_ordered(institute_id=institute_id, user_id=user_id)
+    }
+    sanger_validated_by_user_by_case: Dict[str, List[str]] = {
+        case_variants["_id"]: case_variants["vars"]
+        for case_variants in store.validated(institute_id=institute_id, user_id=user_id)
+    }
 
-    # Retrieve a list of ids for variants with Sanger ordered grouped by case from the 'event' collection
-    # This way is much faster than querying over all variants in all cases of an institute
-    sanger_ordered_by_case = store.sanger_ordered(institute_id, user_id)
     unevaluated = []
+    evaluated_by_others = []
 
-    # for each object where key==case and value==[variant_id with Sanger ordered]
-    for item in sanger_ordered_by_case:
-        case_id = item["_id"]
+    for case_id, var_ids_list in sanger_ordered_by_user_by_case.items():
         # Get the case to collect display name
         CASE_SANGER_UNEVALUATED_PROJECTION = {"display_name": 1}
         case_obj = store.case(case_id=case_id, projection=CASE_SANGER_UNEVALUATED_PROJECTION)
@@ -588,36 +642,20 @@ def get_sanger_unevaluated(store, institute_id, user_id):
             continue
 
         case_display_name = case_obj.get("display_name")
-
-        # List of variant document ids
-        varid_list = item["vars"]
-
-        unevaluated_by_case = {case_display_name: []}
-        for var_id in varid_list:
-            # For each variant with sanger validation ordered
-            variant_obj = store.variant(document_id=var_id, case_id=case_id)
-
-            # Double check that Sanger was ordered (and not canceled) for the variant
-            if (
-                variant_obj is None
-                or variant_obj.get("sanger_ordered") is None
-                or variant_obj.get("sanger_ordered") is False
-            ):
-                continue
-
-            validation = variant_obj.get("validation", "not_evaluated")
-
-            # Check that the variant is not evaluated
-            if validation in ["True positive", "False positive"]:
-                continue
-
-            unevaluated_by_case[case_display_name].append(variant_obj["_id"])
+        unevaluated_by_case, evaluated_by_others_by_case = _get_unevaluated_variants_for_case(
+            case_obj=case_obj,
+            var_ids_list=var_ids_list,
+            sanger_validated_by_user_by_case=sanger_validated_by_user_by_case,
+        )
 
         # If for a case there is at least one Sanger validation to evaluate add the object to the unevaluated objects list
         if len(unevaluated_by_case[case_display_name]) > 0:
             unevaluated.append(unevaluated_by_case)
 
-    return unevaluated
+        if len(evaluated_by_others_by_case[case_display_name]) > 0:
+            evaluated_by_others.append(evaluated_by_others_by_case)
+
+    return unevaluated, evaluated_by_others
 
 
 def export_gene_variants(